The preparation of poly-ether-ether-ketone/bioactive glass (PEEK/BG) composite scaffolds using laser powder bed fusion (LPBF) has enormous clinical potential. However, ensuring the desired accuracy and reproducibility of composite scaffolds during the LPBF process remains a significant challenge. Therefore, a thorough understanding of the relationship between the crystallization behaviors and the scaffold warpage during the LPBF process is crucial. To address this challenge, this study systematically investigates the isothermal crystallization kinetics of PEEK/BG composites and their relationship with scaffold warpage. The results reveal that the crystallization rates of pure PEEK and PEEK/BG composites decrease as isothermal crystallization temperature increases. Additionally, BG significantly suppresses the isothermal crystallization kinetics of PEEK, resulting in a 250% increase in the half-crystallization time (t1/2) of PEEK/25 wt% BG at 316 °C relative to pure PEEK. Extrapolating the t1/2 using the Hoffman-Lauritzen model can obtain the optimal powder bed temperature (Tb) for each powder in LPBF. Pure PEEK and PEEK/25 wt% BG Diamond scaffolds are printed at the respective inferred Tb (330 °C and 323 °C) and their warpage degrees are compared to that of the pure PEEK scaffold printed at 323 °C. The results demonstrate that raising Tb from 323 °C to 330 °C and adding 25 wt% BG are both effective methods to reduce the scaffold warpage by slowing down the crystallization kinetics of PEEK, resulting in reductions of 57.8% and 50.6% in warpage degree respectively. Furthermore, the incorporation of BG successfully tackles the challenge of simultaneously preventing warpage and secondary sintering in pure PEEK printing. Overall, this study offers a deep comprehension regarding the relationship between crystallization kinetics and scaffold warpage, which is crucial for achieving the reproducibility with desired accuracy of LPBF-printed biological scaffolds for clinical applications.